To use the manual patch, you will need to add/update a registry key via RegEdit.
The path to the key is: HKEY_LOCAL_MACHINE\SOFTWARE\Joymax\Silkroad
The name of the key is: InstallPath
The key needs to be a "String Value". The contents of the key is the path to your CSRO folder.
Here is an image of what RegEdit should look like. Your path to CSRO will be different than mine and don't worry about the other keys.
Once you have that key, make sure to not have any other Silkroads open and run the manual patcher as admin. It should update fine after that! I took a look at why the manual patcher was failing and saw it needed that registry key. I just updated mine using this and it works fine.